True the header image size is controlled by the theme, unless you remove it from the theme. I created a script that does some dynamic resizing like on the Wp-twentlyeleven script, as the window gets smaller so does the space between elements and eventually the entire thing shrink into one flex column so it still works well on mobiles (all of this controlled by some css styles to prevent a huge headache in debugging of course).
I avoided the header image width problem in the vanilla wordpress by simply not attaching the width and weight attributes to the image (or to the div in the case of using a background image for the header) This allows me to place the header at 100% width inside a more flexible frame (in the case of the one I'm working on now it's 100% width of the sites master container making it fill up as much as possible.
I'm not sure how Wp-twentyeleven does it be the end effect is very similar. I actually initially noticed your slider didn't resize when testing it on a blog running wp-twenty eleven (my go-to plugin test blog).
Perhaps the solution is simler than it lets on. If you place an option in the settings for this then you could simply not output all the sizes (or, probably display the width as 100% and the height as a value generated to keep the aspect ratio correct, thats some simple jquery to do). This would allow people who have flex themes the freedom to use it full width all the time, and those with traditional static width theme still use it as they are now. One additional thing this might require is tweaks to the nivo slider as well, but they should be pretty basic.
Overal this flex theme, while support as low as the original iphones 320px width, is really designed for older computer or smaller monitors, you can have that extra spacing with a modern 1080p monitor, but most of out clients are running rather outdated hardware. This solves two problems at once, you get a mobile compatible version - which they like, and we make it look good and easily readable on their 1024 monitor.